The idea that has been told to us is that when you do your research of a new 'entity' you can either choose to move up the tree to a new ship type, or you can research a variant of the current type, which would give you a ship with a faster hyper speed, or maybe some more weapons, or a larger cargo capacity etc.

However, this would be locked in at research and would not be able to be changed later - you'd have to do more research on another leaf of the tree to get different stats.

Taking an existing ship and making individual changes to it, if it is allowed at all, would be in the last stages of research and a long way away.